James Wood, 34, and Tanika Bromley, 33, will remain behind bars after their matters appeared in Bundaberg Magistrates Court in southern Queensland.
They have been charged with murder and two counts each of interfering with a corpse.
A police search will focus on locating Pheobe's remains after resuming on Friday, with investigations indicating she may be in a national park near Bundaberg.
"Whilst we always hoped to find Pheobe alive, our investigation ... quite clearly showed us that that was not going to be a viable outcome," Detective Inspector Craig Mansfield said.
Wood and Bromley were arrested on Thursday night, three weeks to the day after Pheobe missed a flight and vanished.
They've been remanded in custody ahead of their next court appearance on August 11.
Locals gathered outside court in Bundaberg, with one holding up a sign in support of the missing teen's shattered family.
Pheobe was last seen near Bundaberg airport about 8.30am on May 15 after booking a trip to Western Australia to see her boyfriend.
Police allege Wood and Bromley drove Pheobe close to the airport in a grey Hyundai but no one exited the car.
Pheobe was allegedly murdered and her body moved more than once from the Good Night Scrub National Park, an hour's drive from the airport.
Police previously searched the park extensively, saying their investigations indicated evidence may have been moved before officers arrived.
However, items found in the park were seized for forensic information.
Police suspect Pheobe's remains are located in the national park, with phone data leading officers to focus on the area.
"We're back to a particular area where we are suspecting that we may locate Pheobe, but again, it is a broad, unforgiving, large area," Det Mansfield told reporters.
"We hope that we'll have a resolution over the coming days."
Police believe they understand the motive for Pheobe's murder, the detective said.
Wood's SUV was seized by police for forensic examination.
He had been living in the vehicle after the Gin Gin property he shared with Bromley and Pheobe was declared a crime scene following the teen's disappearance.
"There is a vehicle that we believe Pheobe was transported in, but I will not disclose that at this point in time," Det Mansfield said.
The community is rallying around Pheobe's family as they try to comprehend their loss.
Pheobe's mother Kylie Johnson documented the heartbreaking toll of her daughter's disappearance, regularly sharing social media updates.
She had gone on Facebook to mark three weeks since Pheobe's disappearance, only to return minutes later after receiving a devastating police update.
"Our world has just been shattered into the most horrific place I've ever been," she wrote on Thursday night.
"I need my baby home to put her to rest! I'm absolutely begging anyone that knows anything to come forward.
"We need to put her to rest, we need to put her to peace."
Wood and Bromley had earlier been charged with unrelated weapons offences.
Police allegedly found a shortened firearm, ammunition and two replica handguns during a search of Bromley's grey Hyundai and further ammunition in the pair's Gin Gin home.
Det Mansfield said he could not speculate on whether the weapons located were involved until Pheobe's body was found.
The tragedy would have cut deep in the tight-knit Gin Gin community with a population of about 1100, Queensland Premier David Crisafulli said.
"But at the heart of it is a young girl who has had her life taken away from her, and that's deeply deeply troubling."
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